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| Status |
Public on Sep 15, 2013 |
| Title |
eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Transcription factors and DNA regulatory binding motifs are fundamental components of the gene regulatory network (GRN). Here, by using genome-wide occupancy profiling of master regulators of MyoGenesis (MyoD and MyoGenin), we show their extensive occupancy in the extragenic enhancer regions coinciding with RNA synthesis (i.e. eRNA). In particular, multiple regions coding for eRNAs were observed within regulatory region of MYOD1, including previously characterized Distal Regulatory Regions (DRR) and Core Enhancer (CE). While CERNA enhanced RNA polymerase II (PolII) occupancy and transcription at MYOD1, DRRRNA acted in trans to activate the downstream MyoGenic GRN. The deployment of transcriptional machinery to appropriate loci is contingent on chromatin accessibility, a rate-limiting step preceding PolII assembly. By nuclease sensitivity assay, we show that eRNAs increase genomic access to the transcriptional complex at defined regulatory regions. In conclusion, our data suggest eRNAs establish a cell-type-specific transcriptional circuitry by directing chromatin-remodeling events.
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| Overall design |
Examination of MyoD and MyoG binding events and production of RNA at the enhancer sites during myogenic differentiation. We performed RNAi against enhancer-derived RNA (DRRi) which resulted in reduction of chromatin accessiblity and RNA polymerase II occupancy at defined regulatory elements. In complementary experiments, overexpression of DRR-RNA (pHAN_DRR1.2) resulted in early activation of MyoG. GFPi and GFP overexpression (pHAN_GFP) were used as control in these experiments, respectively.
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| Contributor(s) |
Mousavi K, Zare H, Dell'Orso S, Grontsved L, Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V |
| Citation(s) |
23993744 |
| Submission date |
Jul 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hossein Zare |
| E-mail(s) |
hzare@mail.nih.gov
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| Organization name |
NIH
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| Street address |
5o South Dr #1347
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| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA213621 |
| SRA |
SRP028299 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE49313_DRRi_GFPi_cds_exp.diff.txt.gz |
909.1 Kb |
(ftp)(http) |
TXT |
| GSE49313_PhanDRR1.2_PhanGFP_cds_exp.diff.txt.gz |
922.5 Kb |
(ftp)(http) |
TXT |
| GSE49313_RAW.tar |
1.7 Gb |
(http)(custom) |
TAR (of BED, BIGWIG, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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